Sonic Atlantis
by Dr. William C.R
Summary: My first ever FanFiction piece. An alternate universe piece using elements of the various Sonic universes with a twist. The twist will be revealed in upcoming chapters. Constructive criticism is encouraged.
1. Chapter 1

Disclaimer: Sonic the Hedgehog and all related characters and properties, are ©SEGA Enterprises, Archie Comics and DiC Animation. All location and events depicted here are fictional.

**Chapter 1:**

It was a dark and stormy night. Spot light beams broke through the blackness in the sky as the Egg-Charier traveled through the storm. Behind it, a small blue biplane approached, fighting the furry of the storm. Sonic the Hedgehog, wearing a brown backpack, held onto the wing of a biplane. It was piloted by a two tailed fox, and they closing in on their target. Their mission was nothing new; foil the plans of the evil Dr. Eggman, or Dr. Robotnik depending on the name he was using that day, and protect their home from emanate destruction while saving it's inhabitants from enslavement. They received a scrambled communication from the rest of the team, who has already infiltrated the flying fortress.

"We're in position. You guys ready," the feminine voice crackled through the radio, "We only have one shot at this."

"Born ready Sall Gall," said a confident Sonic, smirking as he said it.

The fox was obviously disturbed by all the lightning and thunder happening around him. The turbulence didn't help much either.

"Tails," Sonic said to the fox, "Pull it together, scaredy fox! We have a mission to complete!"

"G-Got-cha. Starting ap-proach."

The little fox fought with the controls to keep the plane on course, and his eyes open. The approach triggered the automated alarms on the gigantic aircraft-carrier and Eggman's robot minions were on deck in no-time.

The alarm reaches the helm and caught the eye of the Doctor's assistant, Snively. The man was a short fellow with a long nose, little hair, and green uniform. He tuned to a large fat man wearing blue eye-glasses and wearing an equally flamboyant uniform, if not more.

"Robotnik! We have company!", shouted the assistant as the red sirens went off.

"What did I tell you about that name, Snively?", responded the Doctor with anger in his voice.

"To never mention it in you presence ever again…"

The little man sank back into his chair as he said it.

"Precisely! Why did I even create this alias if no one is going to respect it! Now for the sake of your ruler, go see about that alarm!"

"That is what I was trying to tell you, Sir. Intruders are approaching the Charier! A small blue biplane is approaching at top speed. That could only mean one thing!"

"Yes Snively," said the Eggman with an evil smile, "it's game time."

The Eggman's craft was put on full alert at the blue hedgehog leaps from the plane to _greet_ the oncoming robots. Cannons fire relentlessly upon the little blue aircraft as it bobbed and weaved through the storm. Needless to say, Tails didn't like being the bait. Sonic, on the other hand, seemed to enjoy the excitement that converged on the main deck.

The robots gathered for an attack. "Priority One, apprehend rebel resistance by order of the Eggman, Priority One,…"

"Nice to see you have your priorities in order, fellas. Now let's have some fun. Try to keep up this time." While the blue bomber revved up to spin into action, Sally and the team are getting their chance to move in. A brown ground squirrel dressed in a blue vest and ankle boots watch from the vents for the robots to pass.

"Ok, coast is clear…" She motioned for the other two to follow.

A rabbit with robotic limbs emerged from the vents, soon followed by a skittish coyote in a blue French styled uniform. The one in the uniform suddenly stops to say,

"I am thinking it is a good idea if I just stay right here."

"Sure Antoine," said the ground squirrel, "and when the killer robots come back I'm sure…"

"On second thought, maybe I should be going with you. Safety in numbers."

The rabbit rolled her eyes muttering, sarcastically, "Our _brave_ hero…"

The team made their way through metal clad halls lined with monitors and blinking lights. Sally then pulled a small hand-held device out from the inside of her boot. Whispering into the device, she said, "Nicole, can you show us the layout again?"

"Affirmative." confirmed Nicole, and a holographic image of the Egg Carrier projected from the small device. A blinking dot showed their current positions, Sonic's, Tail's, and a sixth. Wait, a _sixth_ dot!

"Qui est cela," muttered Antoine to himself.

"I didn't know anyone else was come'n on this mission," asked the rabbot.

"No, Bunnie, I don't think I asked anyone else."

"Then who is that?"

Elsewhere on the ship, a voice called out."

"Sonikku…"

The call rang through the dark hanger like a bell. No answer was returned. "Drat," she thought to herself, "where could that hedgehog be?"

(Step… Step…Step…)

She heard footsteps coming closer. "I've got you now.," she thought.

"You're not running away this time!" She charged, bringing down her big mallet at the dark figure.

"Hey, what the…," the dark figure cried out as the hammer came down. To bad it wasn't Sonic's voice.

"Amy, what are you doing here!"

The voice was of Knuckles, a wild Echidna known known for his treasure hunting and short temper.

"Knuckles! I wasn't looking for you! Where is Sonic?"

"Why would I know?"

"Well, could you help me find him?"

"You know, I have more important things to do besides chase down the blue blur for you. Now if you don't mind," he said walking past her, "I have an important job to do."

"You're not working for Robotnik again, are you?"

"No, I'm not! I'm here to retrieve the master emerald and return it to it's rightful place."

"The Master emerald is on this ship?"

"Of course! What do you think has enough power to drive a Chaos Engine big enough to fly this thing? Now if you don't mind…," leaving the girl alone in the hanger. She would now be alone, on a ship full of diabolical machines, each crafted and programmed to maim and kill her.

As she pondered this, a cold chill goes down her spines.

"Knuckles, wait! I'm coming with you!"

Meanwhile, a second party was also looking for the master emerald. A party of one. It was a single, female bat with a fetish for shiny rocks and gems. She observed the two as they exited the hanger. Silently, she followed them, knowing they would lead her to her heart's fondest desire.


	2. Chapter 2

**Chapter 2:**

Outside, Sonic's fight was starting to take a toll. He panted as the bots surrounded. As the situation seemed hopeless he raised his arms into the air in surrender. He looks up towards the sky.

Tails sees the signal and starts his approach. They had everything planned. They were going to take the bots out quick and easy. The plain rushed down the runway unnoticed by the mob of bots focused on Sonic. And with a smirk and a jump flip, he rises just high enough to avoid the biplane now plowing through the mob of bots.

The biplane was stopped by the observation tower, punching a hole in the hull of the ship. A hand emerged from the wreckage, "I'm OK! I'm OK!…" The fox then crawled out unharmed. "I guess I forgot the breaks; and the landing gear."

"Let's move quick before the _clean up crew_ shows up." Sonic's statement was followed by laser fire. "To late."

The two made their way through the open hole in the Carrier followed by robots.

Deep in the ship, Amy and Knuckles were getting closer to the master emerald.

"How do you know which way to go?" asked Amy, "I can hardly see where we are."

"Hey, I didn't ask you to follow."

"It was just a question."

"I'm a guardian; I can sense how close I am to the master emerald."

Knuckles suddenly stopped dead in his tracks and sniffed the air curiously. His curiosity quickly turned into anger as he realized they were being tailed.

"Oh, crud." Thought the bat as she flew from her perch, "It looks like I'll have to do this the hard way."

She attacked with a kick. But her cover was blown, and knuckles had plenty of time to anticipate it. He dove away as the bat's sharp toed boots struck the spot where he was once standing. Amy swung her hammer, only to have it be avoided as she tried to knock the bat out flight. Knuckles caught the bat by surprise and pinned her to the wall.

"Rouge, I should have known you'd have something to do with this. Where is it?"

"Me, really, why would I be tailing you two if I already knew where the emeralds were? What's wrong Knukie, don't you trust me?"

"…about as far as I can throw you."

Amy interrupts demandingly, "Where's Sonic?"

Rouge got a glint in her eyes, "Let me go and you'll find out."

Knuckles loosened his grip, allowing Rouge to push him back and make a break for it.

"Hey," Amy cried, "you were suppose to tell us where Sonic is!"

"As if I'd tell you…" called Rouge from down the hall.

Knuckles got back to his feet and started to go after the bat with Amy tailing behind.

"Maybe Rouge knew where Sonic is." she thought to herself.

Elsewhere, Sally had reached an unguarded terminal. The others played roll of lookouts as she prepared Nicole for the task of altering their flight path.

"Nicole, run command _Egg-Hack._"

"Commencing…" confirmed Nicole. The terminal started to come to life as the AI tried to gain access to Eggman's flight computer.

On the brig, Eggman called for his assistant to, "Power up the Chaos Engine!"

"But Sir, it's still in the experimental stages. Shouldn't we run a few more tests before trying anything rash?"

"No, Snively, the conditions are ripe! It's time to show them what this ship was meant to do."

"Yes, sir." Snively tapped on the control panel in front of him. The ship lurched as the engines forced their true power. The affects were felt throughout the whole ship.

Sally and the crew fell the floor. The two lookouts noticed something very strange outside the potholes.

"Oh my stars… Sally Girl, you might want to come see this!" the rabbit urged.

Sally moved to one of the windows, awestruck at what she was seeing.

Outside, the entire ship was engulfed in a strange, pinkish haze. Lightning surged through it like the blood through their vanes as their pulses quickened from fear. The Carrier had entered a realm of perpetual limbo known only as the Void!

Inside the belly of the ship, Rouge had stumbled upon just what she was looking for. Before her stud the master emerald, surrounded by the seven chaos emeralds. Each one glowing like wildfire and pulsing with energy. They were all sealed in air tight glass tubes with a network of wires and gadgets connecting them together. Rouge was only concerned with the emeralds.

"Finally, I found them!"

Knuckles and Amy skid to a stop behind her. "Don't you dare lay a finger on those emeralds!" shouted Knuckles.

"Or you'll what, shake your fists at me?"

"Gerrrrr… I'll show you fists!" The wild Echidna lunged forward towards the bat with his spike clad fists. The bat spread her wings and flew upward, avoiding any kind of contact to her person. Unfortunately, she had forgotten about the emeralds behind her.

Knuckles' fist struck the containment tubs, causing a chain reaction in the Chaos engine. He was then thrown back towards the others as a huge explosion ripped yet another hole into the hull of the ship. It shattered the master emerald into shards and scattered them, as well as the chaos emeralds, down into the Void.

As a result of the engine being completely destroyed, the power for the entire ship was cut off. But this was not the only affects.

Sally, Bunnie, and Antoine felt the ship shake as the explosion accrued cutting off all power. Strangely enough, this also drained Nickole.

"Tonight just keeps going from bad, and worse." Sally muttered to her comrades.

Sonic came rushing past them with Tails following, and stopping in time. Sonic back tracked to meet up with the others. "What a blast! What did you guys do to the ship?"

"We did no thing!" exclaimed Antoine, "It's a black-off!"

"You mean black-out, right?"

"That's what I say, black-off!"

With the power out and the engines off, the ship started to descend.

"Sonic," cried Tails, "I think we should get going. Hay, where's the Void going?"

Outside the ship, the pink haze of the void seemed to fade away returning to the raging storm that was once there. And it wasn't long before the ship started to do the same thing.

"Sally, got a plan?" Sonic asked.

"I don't know. Nicole's unresponsive and I have no clue as to what's going on anymore oh…" Sally started to sink into the floor of the ship!

Sonic quickly snatched her up, but only to find the others were now missing!

Sonic new he had to find safety, but where? He sped down the fazing halls and disappearing corridors, using every trick he knew to evade the loss of ground while keeping hold of his damsel in distress. He was to busy trying to find footing that he didn't notice the pipes that were materializing before his feet. He tripped, and the world seemed to fall into slow motion.

Sally flew out of his arms. Sonic's arms stretched out as he fall to the floor helpless. She Skidded off the ground before looking back falling through it into the darkness of the storm.

And just like that, she was gone. Sonic laid there dumbfounded as to what had just happened. He could feel the ground below him grow fainter, eventually giving way. He fell into dark clouds and lightning.

Back on the brig, The effects seen throughout the ship were not felt. This did not surprise the Eggmen. He had planned this whole situation. They made adjustments to the ship prier to the experiment, although the loss of the Chaos engine was not part of the plan. He and Snively strapped themselves into their chairs and prepared for the inevitable crash.


	3. Chapter 3

**Chapter 3**

Sonic fell through the gray skies. He could start to see the sea rushing towards him. Out of the corner of his eye, he caught a glimpse of a small yacht. On it was a boy, but he couldn't quite make him out before he plunged under the waves. When he finally reemerged, the boy had jumped off and was trying to swim towards him.

Not the wisest of decisions. A wave caught the boy and he went submerged for a long period of time. Sonic knew he had to do something. The hedgehog reached behind him into his backpack and pulled out a glowing gold ring.

As the boy blacked out under the waves, he could see the silhouette of a creature, the light from the ring breaking through the dark water.

When the boy woke up, he was back on the yacht. Before him stud what looked like a blue hedgehog in sneakers and gloves.

"Are you OK?" it asked him.

This surprise was too much for the boy to take, and he fainted once again. Sonic was about to help him up when he heard others coming up the side of the boat. Since he had no idea where he was, his gut told him to lay low until they got back to shore. He went to a spot out of sight below deck. The commotion outside was muffled by the now dying storm.

When the boy awoke, they were docking at the harbor. He was lying below deck, still in his wet clothes. The past events felt almost like a dream.

An old man came below deck. "Chris!" he said, "You're awake! You have been out for hours. I thought Dr. White told him to stay below deck?"

"I did, but there was this storm and…" Chris paused to contemplate the events of the day, "On second thought, you'd never believe me."

"Come on, let's get you home." the old man said helping the boy to his feet, "We can talk all about it at home."

As the two left the ship, Sonic saw his chance to split. He left in a blue streak, unnoticed by anyone else. Nothing he passed seemed familiar. He could tell it was a city, but where was he? It was getting dark, so he would have to find his friends and fast.

Later that night, Sally was just waking up from her ordeal. She remembered falling through the storm and hitting the water, but everything after that was a blur. She staggered to her feet.

She could see a small ledge ahead of her beyond that was a road; and beyond that, a city. She was amazed, a city not claimed by Eggman's rule. How could this be? She hoisted herself up onto the ledge and started to cross the road. As she did two lights raced down the road. She looked to her side and froze like a deer caught in headlights. A juiced up formula one car barreled down the road towards her. Luckily, she was whisked out of the way into the safety of an ally by Sonic, who found her in the nick of time.

"That was a close one." Sonic said, "Wow, two saves in one night!"

"Thank you Sonic. Wait, who else did you save?"

"Some kid I saw doing the belly up. By the way, any idea where we are."

"Well," Sally said checking the pouch on the side of her boot, "let me check Nicole… Oh no!"

"What's wrong, Sal?"

"I can't find Nicole! It must have fallen out when I fell through..."

"The floor, right, while the Carrier was pulling a Houdini."

"This is getting to be too much."

"I bet- ya Mr. Speedy knows something about where we are." Sonic said.

"Wait, shouldn't we…" her words were too late, Sonic had already bolted after the car.

"…stick together." She let out a heavy sigh. "There he goes again."

Sonic barreled down the streets, hoping to catch up with the wise guy who almost made road kill of his Sal Gal. He was at top speed when he overshot his objective. The driver saw a streak of blue light flash by his driver side, extending for miles.

"What in the world was that?" thought the driver as he stopped his car. A voice came through his headset.

"Then why did you stop! You know we have the entire length of the road blocked off for the trial, just open her up already."

"There's something else on the road here, and it was fast."

Sam Speed looked up to see the blue blur coming back towards him.

"Crew, it's coming back, and it looks ticked!"

Sam put on the petal to the metal as the two passed for a second time. Sonic did a drifting u-turned and pursued the car. Sam had to concentrate. He had to finish the trial and the _thing_ had already cost him time. Sonic came up beside the driver-side window.

"So it's a race. Fine, Speed accepts your challenge." The car sped up to outrun the blue hedgehog. Sonic wasn't about to be outrun, or ignored, by the likes of this guy. He caught up in no-time and hoped onto the hood.

"Hey!" yelled the driver, "Didn't anyone tell you not to ride on top of racecars!?"

"Didn't your mom tell you to look out for pedestrians!?" the hedgehog snapped back.

Sam hit the turbo bust, sending sonic flying over the roof and landing behind it on the road. Sonic realized this guy wouldn't give him any answers, but he wasn't one to loose a race. He got to his feet and showed his new rival what real speed looked like. The resulting shockwave form the sonic boom caused the car to swerve and skid to a stop. An aggravated Sam Speed got out of the car and stared at the trail of fire that extended off into the distance. He threw his helmet down at his most recent loss.

His headset crackled again, "Sam, What happened!"

"I don't want to talk about it."

"But what was that thing. Did it hit mock…?"

"I said I don't want to talk about it! Just set up for another run-through."


	4. Chapter 4

**Chapter 4**

In another end of the city, Knuckles paces on the shore. Amy is standing near by facing the city. It is still dark out.

"So where do you think we are?" asked Amy.

"I don't know, but we'll never find out just standing here."

Knuckles starts walking towards an open sewer drain and starts to climb into it.

"Sonic!" She starts calling towards the city. Knuckles quickly mutes her with his mitt placed over her mouth.

"Shhh!" he whispers, "You want to get us found! For all we know, this could be a Robotnik outpost. What do you think would happen it a squad of robots found us."

Amy gives him a cold look and draws out her hammer, causing him to recoil his hand immediately.

There scuffle is interrupted by a blinding light from a vehicle on the road. They didn't take time to make out their forms, knuckles just grabbed Amy's arm and darted into the sewer drain. They were followed by two uniformed officers with flashlights who emerged from their police car.

"What in the good name was that!?"

"I don't know? But whatever it was, I think it's out of our jurisdiction!"

Meanwhile, Sonic and Sally were looking for the others.

"We have to find the others." Sally says to Sonic, "If I still had Nicole, we would be able to find them easily. I shouldn't have,"

"Sal, it was an accident. Who knew the entire ship would disappear? Stop blaming yourself." A storm rolled in and started pouring.

"What's with tonight and water, anyway?" Sonic said. "I think I see a place up here."

They crept up through the gate of the estate and made their way to the garage.

"Sonic, I don't think this is right."

"Sal, it's either this or rain." He stud on a garbage can to open the side window. "We'll just say we needed to get out of the rain."

"For once, I guess you're right." Said Sally as the two entered the garage.

Just as the two were inside, a van pulled up in the driveway. Dr Thorndyke Sr., the old man, exited the car. "What a storm! Just came out of nowhere!" he said holding a newspaper over his head and a cup of coffee in his hand. He went to unlock the garage door. Sonic and Sally, hearing the door, ducked under the bed.

"So Chris," the old man started, "you still feeling alright. What exactly happened out there."

"I, um… fell overboard."

"Well, be more careful next time. I'll see how Ella is doing with supper, You're sure you're ok?"

"Yea, I'm fine."

The old man left the garage and Chris turned on his grandfather's small television. The news was reporting on what was a huge island off the coast of Station Square, Florida.

Sally, now fixed on the screen muttered, "That's Mobius!".

Chris perked up. "What was that?"

Both Sonic and Sally hid deeper into the dark corner under the bed. Chris got off the bed and started looking around.

"Hello?" he warily called out.

Sonic, recognizing the boy, started to crawl from under the bed.

"_What are you doing?_" Sally whispered to Sonic sternly.

"He already knows we are here. Besides, I think he owes me."

Sonic stepped into plain view of the boy.

"_It's you!_" muttered the boy.

"Please don't bolt kid," said the hedgehog, "we're just look'n for a place to wait out the storm. We, didn't know this was you're pad."

"We?" asked the boy, "Who else is here."

Sally saw this as her cue to reluctantly step out into the light. This was followed by the sound of the door.

"Chris, how do you feel about roast beef?" The grandfather turned taking a sip of his coffee, just to loose it in a spit take. The correspondent on the news echoed the sight.

"And just recently, sightings of strange, oversized animals have been springing up all over the city. Officials have yet to report if this has any connection to the sudden occurrence of an island off our shores or not. More on that at eleven…"


	5. Chapter 5

Chapter 5:

**Chapter 5:**

The awkward moment seemed to stretch forever until Chris broke to silence.

"Well, you always said I should have a pet."

"Excuse me?!" Sally said insulted, "We are not pets. Just give us a minute to explain; although there is a lot we don't know ourselves. We arrived here, wherever here is, when we infiltrated one of Robotnik's ships and…"

Both Sonic and Sally's eyes grew wide when she realized what danger they brought with them.

Else where, just off the coast, the huge Egg Charier lay crashed and partly submerged. All power was out throughout the ship.

"Snively," Snapped the Eggman, "turn on the emergency backup generators. They should be working now. And let's shed some light on our current location."

As he said this he stepped out of their protective room to inspect the damage. Flood lights started to light the bow of the Charier revealing an almost gruesome sight. The robots onboard had fused to the steel structure of the ship. Inactive robotic limbs reached from the paneling of the ship and other structures. And as before, Eggman was not surprised or enraged one bit, he was actually smiling. His sights were on the coast in the distance and the lights of the city within it. He took a deep breath and muttered, "It's good to be back."

Snively come over the intercom saying, "Doctor, we have incoming intruders."

"Cloak the ship." , was his response.

The faint sound of helicopters was faint in the distance.

"Sir, we have a problem… I can't cloak the ship with the power of the master emerald."

"WHAT!" snapped the doctor, "WHY NOT?!"

"...because there is not master emerald, sir. It's gone. There's also a massive hole in the engine room."

The Eggman let out a frustrated sigh. "Then well do this the hard way. Initiate a 'welcome party' and meet me back in the beige, we need to find that emerald!"

The center of the deck split apart and a large, bird like aircraft rose from the hanger and lifted off immediately towards the growing sound of the copters.

As he returned, Snively opened another hanger releasing more robots ordered to salvage the robots fused to the deck. Both hangers were protected from the incident in much the same way the brig was.

Meanwhile, under the streets of the city, Amy and Knuckles were moving onward.

"We've been walking for hours, Knuckles." pleaded Amy "Can't we take a rest?"

"You can take a rest, I'm moving on." said Knuckles.

"What! And leave me all alone down here! There could be bots down here!"

"Yea, you can fend for yourself."

"Sure, but…"

Just then a huge explosion from above shook the sewer. Amy slipped into the sludge.

"Eeew! And this was my good dress!"

Knuckles immediately climbed to the manhole to see what the commotion was about. They came out just behind a huge group of police officers and GUN team looking up at an air fight between two GUN helicopters and a huge robotic bird like jet. One chopper had crashed and was lying in the street. The choppers were returning to base after being ambushed. Knuckles recognized the robot as one of Eggman's designs.

"Amy!" he shouted below, "We got trouble. Grab your mallet."

Back at the Thorndyke's garage the attack was breaking news. The news anchor said "Miraculously, no-one was killed in the attacks yet. But two choppers are still unable to break free from the unknown jet attacks. And the origins of this strange, bird like jet are still unknown." In the backdrop behind the anchor, the air fight continued.

"Wait!" called Sally as Sonic started out the door, "We need a plan. We don't know exactly what were up against here."

"Well, didn't you hack Robutnick's schematics before the mission?"

"I did, but they are on Nicole."

"I got a laptop in my room," spoke the young boy "will that help."

"Sure," said Sally "but I don't think it'll be enough."

"I think it's all we got, Sal." said Sonic.

Chuck lifted the tarp off an old restored car at the other end of the garage, pulling two headsets from the dashboard.

"You may need these."

He handed them two headsets.

"So we can stay in contact." He continued to pull the tarp from the car. Chris came back in with a laptop under his arm.

"Toss it in the back Chris."

"Wait," said Sally, "you don't think your coming, do you? That thing is dangerous!"

"Dangerous or not, we need their help." said Sonic, "Besides, they know the area better than we do."

"I guess your right…" Sonic helped her into the car.

"Just follow the car, Sonic." said Grandpa Chuck, "We'll lead the way."

The good doctor sped out the garage with the blue blur close at hand.


End file.
